Feral populations of cultivated crops have the potential to function as bridges and reservoirs that contribute to the unwanted movement of novel genetically engineered (GE) traits. Recognizing that feral alfalfa has the potential to lower genetic purity in alfalfa seed production fields when it is growing in the vicinity of foraging pollinators in alfalfa seed fields, industry has established production standards to control feral plants. However, with the commercialization of GE glyphosate-resistant (GR) alfalfa and the need to support the coexistence of both GE and conventional production, effective methods to control transgenic feral alfalfa need to be developed. Therefore, a study was conducted in 2012, 2013, and 2014 to determine the effect of several synthetic auxin herbicides on seed development in GR alfalfa. GR alfalfa, var. Genuity (R44BD16), was treated with dicamba, 2,4-D, triclopyr, and aminopyralid when alfalfa plants contained green seed pods. Two weeks after herbicide application, plants were harvested, air dried, and seed yield, seed germination, and seedling emergence from the soil were determined. In 2013, dicamba, triclopyr, and 2,4-D decreased alfalfa seed yield per plant compared wih nontreated plants, whereas in 2014, all four herbicides decreased alfalfa seed yield per plant 24 to 49% (by weight) compared with nontreated plants. The same trend was evident in 2012, but seed yield was variable and was not significantly different among treatments. Seed germination averaged 43, 50, and 72% in 2012, 2013, and 2014, respectively, and was not affected by the four herbicides applied at early pod-fill stage. However, seeds harvested from plants treated with dicamba, 2,4-D, and triclopyr often produced deformed and abnormal seedlings, and when planted in soil, frequently failed to emerge. The combined effects of dicamba, 2,4-D, and triclopyr in reducing seed yield, seedling emergence, and seedling growth could contribute to managing feral alfalfa populations.